# periodic boundary conditions along all three dimensions boundary p p p # Set neighbor skin variable neigh_skin equal 2.0*${_u_distance} variable neigh_skin equal 2.0*1 neighbor ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.920081198215485*${_u_distance} variable latticeconst_converted equal 3.920081198215485*1 lattice fcc ${latticeconst_converted} lattice fcc 3.92008119821549 Lattice spacing in x,y,z = 3.9200812 3.9200812 3.9200812 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (39.200812 39.200812 39.200812) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (39.200812 39.200812 39.200812) create_atoms CPU = 0.001 seconds variable mass_converted equal 195.078*${_u_mass} variable mass_converted equal 195.078*1 kim interactions Pt #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Pt__MO_601539325066_001 pair_coeff * * Pt #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 195.078 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 60240.0312503115 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 60240.0312503115/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 60240.0312503115/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 60240.0312503115/(1*1*${_u_distance}) variable V0_metal equal 60240.0312503115/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 60240.0312503115*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 60240.0312503115 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 0.1*${_u_time} variable Pdamp_converted equal 0.1*1 # create initial velocities consistent with the chosen temperature velocity all create ${temp_converted} 17 mom yes rot yes velocity all create 313.15 17 mom yes rot yes # set NPT ensemble for all atoms fix ensemble all npt temp ${temp_converted} ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_u_energy} variable etotal_metal equal etotal/1 variable pe_metal equal pe/${_u_energy} variable pe_metal equal pe/1 variable T_metal equal temp/${_u_temperature} variable T_metal equal temp/1 variable V_metal equal vol/(${_u_distance}*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*1*${_u_distance}) variable V_metal equal vol/(1*1*1) variable P_metal equal press/${_u_pressure} variable P_metal equal press/1 fix avgmyTemp all ave/time 5 20 100 v_T_metal ave running start 1000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 1000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 1000 # extract fix quantities into variables so they can be used in if-else logic later. variable T equal f_avgmyTemp variable P equal f_avgmyPress variable V equal f_avgmyVol # set error bounds for temperature and pressure in original metal units (K and bar) variable T_low equal "313.15 - 1.0" variable T_up equal "313.15 + 1.0" variable P_low equal "0.0 - 5.0" variable P_up equal "0.0 + 5.0" # print to logfile every 1000 timesteps thermo_style custom step etotal v_etotal_metal pe v_pe_metal temp v_T_metal vol v_V_metal press v_P_metal thermo 1000 # Run a simulation for at most 2000*1000 timesteps. At each 1000th time step, check # whether the temperature and pressure have converged. If yes, break. label top variable a loop 2000 run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM Project: doi:10.1007/s11837-011-0102-6 @Article{tadmor:elliott:2011, author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker}, title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels}, journal = {{JOM}}, year = 2011, volume = 63, number = 17, pages = {17}, doi = {10.1007/s11837-011-0102-6} } - OpenKIM potential: https://openkim.org/cite/MO_601539325066_001#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1981926 ghost atom cutoff = 8.1981926 binsize = 4.0990963, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.481 | 5.481 | 5.481 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -22918.117 -22918.117 -23079.988 -23079.988 313.15 313.15 60240.031 60240.031 2870.3265 2870.3265 1000 -22747.403 -22747.403 -22909.594 -22909.594 313.77029 313.77029 60908.743 60908.743 1670.8042 1670.8042 Loop time of 10.7243 on 1 procs for 1000 steps with 4000 atoms Performance: 8.056 ns/day, 2.979 hours/ns, 93.246 timesteps/s, 372.984 katom-step/s 97.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.395 | 10.395 | 10.395 | 0.0 | 96.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.079983 | 0.079983 | 0.079983 | 0.0 | 0.75 Output | 0.00021593 | 0.00021593 | 0.00021593 | 0.0 | 0.00 Modify | 0.20716 | 0.20716 | 0.20716 | 0.0 | 1.93 Other | | 0.04241 | | | 0.40 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 560000 ave 560000 max 560000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560000 Ave neighs/atom = 140 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 314.119315617894, Press = 87.7531685842278 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1981926 ghost atom cutoff = 8.1981926 binsize = 4.0990963, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.481 | 5.481 | 5.481 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -22747.403 -22747.403 -22909.594 -22909.594 313.77029 313.77029 60908.743 60908.743 1670.8042 1670.8042 2000 -22729.098 -22729.098 -22891.264 -22891.264 313.72074 313.72074 60969.917 60969.917 2093.176 2093.176 Loop time of 11.5084 on 1 procs for 1000 steps with 4000 atoms Performance: 7.508 ns/day, 3.197 hours/ns, 86.893 timesteps/s, 347.571 katom-step/s 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.168 | 11.168 | 11.168 | 0.0 | 97.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.080592 | 0.080592 | 0.080592 | 0.0 | 0.70 Output | 0.00010666 | 0.00010666 | 0.00010666 | 0.0 | 0.00 Modify | 0.2078 | 0.2078 | 0.2078 | 0.0 | 1.81 Other | | 0.05176 | | | 0.45 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 577926 ave 577926 max 577926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577926 Ave neighs/atom = 144.4815 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 313.162638228683, Press = 9.45663639452666 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1981926 ghost atom cutoff = 8.1981926 binsize = 4.0990963, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.481 | 5.481 | 5.481 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -22729.098 -22729.098 -22891.264 -22891.264 313.72074 313.72074 60969.917 60969.917 2093.176 2093.176 3000 -22724.882 -22724.882 -22885.137 -22885.137 310.0231 310.0231 60935.86 60935.86 3992.6715 3992.6715 Loop time of 10.7439 on 1 procs for 1000 steps with 4000 atoms Performance: 8.042 ns/day, 2.984 hours/ns, 93.076 timesteps/s, 372.306 katom-step/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.462 | 10.462 | 10.462 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.060844 | 0.060844 | 0.060844 | 0.0 | 0.57 Output | 8.6843e-05 | 8.6843e-05 | 8.6843e-05 | 0.0 | 0.00 Modify | 0.18704 | 0.18704 | 0.18704 | 0.0 | 1.74 Other | | 0.03341 | | | 0.31 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8193 ave 8193 max 8193 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 579156 ave 579156 max 579156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579156 Ave neighs/atom = 144.789 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 313.316290439972, Press = 7.33389792703276 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1981926 ghost atom cutoff = 8.1981926 binsize = 4.0990963, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.481 | 5.481 | 5.481 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -22724.882 -22724.882 -22885.137 -22885.137 310.0231 310.0231 60935.86 60935.86 3992.6715 3992.6715 4000 -22741.346 -22741.346 -22903.979 -22903.979 314.62517 314.62517 60900.896 60900.896 2159.7602 2159.7602 Loop time of 10.5174 on 1 procs for 1000 steps with 4000 atoms Performance: 8.215 ns/day, 2.922 hours/ns, 95.080 timesteps/s, 380.321 katom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.228 | 10.228 | 10.228 | 0.0 | 97.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.060552 | 0.060552 | 0.060552 | 0.0 | 0.58 Output | 9.3596e-05 | 9.3596e-05 | 9.3596e-05 | 0.0 | 0.00 Modify | 0.19084 | 0.19084 | 0.19084 | 0.0 | 1.81 Other | | 0.0377 | | | 0.36 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8193 ave 8193 max 8193 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 579352 ave 579352 max 579352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579352 Ave neighs/atom = 144.838 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" jump SELF break # Write final averaged volume to file if temperature and volume have converged; otherwise wirte a # flag to indicate non-convergence. variable myStep equal step if "${myStep} < 2000000" then "print '${V}' file output/vol_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 60953.3636345758 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0